/* Menus and command line interface for Clustal W  *//* DES was here MARCH. 1994 *//* DES was here SEPT.  1994 */#include <stdio.h>#include <string.h>#include <ctype.h>#include <stdlib.h>#include <stdarg.h>#include <signal.h>#include <setjmp.h>#include "clustalw.h"static jmp_buf jmpbuf;#ifndef VMS#ifndef AIX#define BADSIG (void (*)())-1#endif#endifstatic void jumper(int);static void jumper(int i){        longjmp(jmpbuf,1);}/**	Prototypes*/static void pair_menu(void);static void multi_menu(void);static void gap_penalties_menu(void);static void multiple_align_menu(void);          /* multiple alignments menu */static void profile_align_menu(void);           /* profile       "      "   */static void phylogenetic_tree_menu(void);       /* NJ trees/distances menu  */static void format_options_menu(void);          /* format of alignment output */static void tree_format_options_menu(void);     /* format of tree output */static void ss_options_menu(void);static sint secstroutput_options(void);static sint read_matrix(char *title,MatMenu menu, char *matnam, sint matn, short *mat, short *xref);/**	 Global variables*/extern float    gap_open,      gap_extend;extern float  	dna_gap_open,  dna_gap_extend;extern float 	prot_gap_open, prot_gap_extend;extern float    pw_go_penalty,      pw_ge_penalty;extern float  	dna_pw_go_penalty,  dna_pw_ge_penalty;extern float 	prot_pw_go_penalty, prot_pw_ge_penalty;extern float	transition_weight;extern char 	revision_level[];extern sint    wind_gap,ktup,window,signif;extern sint    dna_wind_gap, dna_ktup, dna_window, dna_signif;extern sint    prot_wind_gap,prot_ktup,prot_window,prot_signif;extern sint	nseqs;extern sint 	divergence_cutoff;extern sint 	debug;extern Boolean 	neg_matrix;extern Boolean  quick_pairalign;extern Boolean	reset_alignments_new;		/* DES */extern Boolean	reset_alignments_all;		/* DES */extern sint 	gap_dist;extern Boolean 	no_var_penalties, no_hyd_penalties, no_pref_penalties;extern sint 	output_order;extern sint profile_no;extern short 	usermat[], pw_usermat[];extern short 	aa_xref[], pw_aa_xref[];extern short 	userdnamat[], pw_userdnamat[];extern short 	dna_xref[], pw_dna_xref[];extern Boolean 	lowercase; /* Flag for GDE output - set on comm. line*/extern Boolean 	cl_seq_numbers;extern Boolean seqRange;  /* to append sequence range with seq names, Ranu */extern Boolean 	output_clustal, output_nbrf, output_phylip, output_gcg, output_gde, output_nexus;extern Boolean output_fasta; /* Ramu */extern Boolean 	output_tree_clustal, output_tree_phylip, output_tree_distances,output_tree_nexus;extern sint     bootstrap_format;extern Boolean 	tossgaps, kimura;extern Boolean  percent;extern Boolean 	usemenu;extern Boolean 	showaln, save_parameters;extern Boolean	dnaflag;extern Boolean  use_ambiguities;extern char 	hyd_residues[];extern char 	mtrxname[], pw_mtrxname[];extern char 	dnamtrxname[], pw_dnamtrxname[];extern char	seqname[];extern sint output_struct_penalties;extern Boolean use_ss1, use_ss2;extern Boolean empty;extern Boolean profile1_empty, profile2_empty;   /* whether or not profiles   */extern char  	profile1_name[FILENAMELEN+1];extern char  	profile2_name[FILENAMELEN+1];extern Boolean         use_endgaps;extern sint        matnum,pw_matnum;extern sint        dnamatnum,pw_dnamatnum;extern sint        helix_penalty;extern sint        strand_penalty;extern sint        loop_penalty;extern sint        helix_end_minus;extern sint        helix_end_plus;extern sint        strand_end_minus;extern sint        strand_end_plus;extern sint        helix_end_penalty;extern sint        strand_end_penalty;extern MatMenu matrix_menu;extern MatMenu pw_matrix_menu;extern MatMenu dnamatrix_menu;static char phylip_name[FILENAMELEN]="";static char clustal_name[FILENAMELEN]="";static char dist_name[FILENAMELEN]="";static char nexus_name[FILENAMELEN]="";static char fasta_name[FILENAMELEN]="";static char p1_tree_name[FILENAMELEN]="";static char p2_tree_name[FILENAMELEN]="";static char *secstroutput_txt[] = {				"Secondary Structure",				"Gap Penalty Mask",				"Structure and Penalty Mask",				"None"	};				                static char *lin1, *lin2, *lin3;static int firstres =0;	/* range of alignment for saving as ... */static int lastres = 0;void init_amenu(void){	lin1 = (char *)ckalloc( (MAXLINE+1) * sizeof (char) );	lin2 = (char *)ckalloc( (MAXLINE+1) * sizeof (char) );	lin3 = (char *)ckalloc( (MAXLINE+1) * sizeof (char) );}void main_menu(void){        int catchint;        catchint = signal(SIGINT, SIG_IGN) != SIG_IGN;        if (catchint) {                if (setjmp(jmpbuf) != 0)                        fprintf(stdout,"\n.. Interrupt\n");#ifdef UNIX                if (signal(SIGINT,jumper) == BADSIG)                        fprintf(stdout,"Error: signal\n");#else                if (signal(SIGINT,SIG_DFL) == BADSIG)                        fprintf(stdout,"Error: signal\n");#endif        }	while(TRUE) {		fprintf(stdout,"\n\n\n");		fprintf(stdout," **************************************************************\n");		fprintf(stdout," ******** CLUSTAL %s Multiple Sequence Alignments  ********\n",revision_level);		fprintf(stdout," **************************************************************\n");		fprintf(stdout,"\n\n");				fprintf(stdout,"     1. Sequence Input From Disc\n");		fprintf(stdout,"     2. Multiple Alignments\n");		fprintf(stdout,"     3. Profile / Structure Alignments\n");		fprintf(stdout,"     4. Phylogenetic trees\n");		fprintf(stdout,"\n");		fprintf(stdout,"     S. Execute a system command\n");		fprintf(stdout,"     H. HELP\n");		fprintf(stdout,"     X. EXIT (leave program)\n\n\n");				getstr("Your choice",lin1);		switch(toupper(*lin1)) {			case '1': seq_input(FALSE);				phylip_name[0]=EOS;				clustal_name[0]=EOS;				dist_name[0]=EOS;				nexus_name[0]=EOS;				break;			case '2': multiple_align_menu();				break;			case '3': profile_align_menu();				break;			case '4': phylogenetic_tree_menu();				break;			case 'S': do_system();				break;			case '?':			case 'H': get_help('1');				break;			case 'Q':			case 'X': exit(0);				break;			default: fprintf(stdout,"\n\nUnrecognised Command\n\n");				break;		}	}}static void multiple_align_menu(void){        int catchint;        catchint = signal(SIGINT, SIG_IGN) != SIG_IGN;        if (catchint) {                if (setjmp(jmpbuf) != 0)                        fprintf(stdout,"\n.. Interrupt\n");#ifdef UNIX                if (signal(SIGINT,jumper) == BADSIG)                        fprintf(stdout,"Error: signal\n");#else                if (signal(SIGINT,SIG_DFL) == BADSIG)                        fprintf(stdout,"Error: signal\n");#endif        }    while(TRUE)    {        fprintf(stdout,"\n\n\n");        fprintf(stdout,"****** MULTIPLE ALIGNMENT MENU ******\n");        fprintf(stdout,"\n\n");        fprintf(stdout,"    1.  Do complete multiple alignment now (%s)\n",                        (!quick_pairalign) ? "Slow/Accurate" : "Fast/Approximate");        fprintf(stdout,"    2.  Produce guide tree file only\n");        fprintf(stdout,"    3.  Do alignment using old guide tree file\n\n");        fprintf(stdout,"    4.  Toggle Slow/Fast pairwise alignments = %s\n\n",                                        (!quick_pairalign) ? "SLOW" : "FAST");        fprintf(stdout,"    5.  Pairwise alignment parameters\n");        fprintf(stdout,"    6.  Multiple alignment parameters\n\n");	fprintf(stdout,"    7.  Reset gaps before alignment?");	if(reset_alignments_new)		fprintf(stdout," = ON\n");	else		fprintf(stdout," = OFF\n");        fprintf(stdout,"    8.  Toggle screen display          = %s\n",                                        (!showaln) ? "OFF" : "ON");        fprintf(stdout,"    9.  Output format options\n");        fprintf(stdout,"\n");        fprintf(stdout,"    S.  Execute a system command\n");        fprintf(stdout,"    H.  HELP\n");        fprintf(stdout,"    or press [RETURN] to go back to main menu\n\n\n");        getstr("Your choice",lin1);        if(*lin1 == EOS) return;        switch(toupper(*lin1))        {        case '1': align(phylip_name);            break;        case '2': make_tree(phylip_name);            break;        case '3': get_tree(phylip_name);            break;        case '4': quick_pairalign ^= TRUE;            break;        case '5': pair_menu();            break;        case '6': multi_menu();            break;	case '7': reset_alignments_new ^= TRUE;	    if(reset_alignments_new==TRUE)		reset_alignments_all=FALSE;            break;        case '8': showaln ^= TRUE;	    break;        case '9': format_options_menu();            break;        case 'S': do_system();            break;        case '?':        case 'H': get_help('2');            break;        case 'Q':        case 'X': return;        default: fprintf(stdout,"\n\nUnrecognised Command\n\n");            break;        }    }}static void profile_align_menu(void){        int catchint;        catchint = signal(SIGINT, SIG_IGN) != SIG_IGN;        if (catchint) {                if (setjmp(jmpbuf) != 0)                        fprintf(stdout,"\n.. Interrupt\n");#ifdef UNIX                if (signal(SIGINT,jumper) == BADSIG)                        fprintf(stdout,"Error: signal\n");#else                if (signal(SIGINT,SIG_DFL) == BADSIG)                        fprintf(stdout,"Error: signal\n");#endif        }    while(TRUE)    {	fprintf(stdout,"\n\n\n");        fprintf(stdout,"****** PROFILE AND STRUCTURE ALIGNMENT MENU ******\n");        fprintf(stdout,"\n\n");        fprintf(stdout,"    1.  Input 1st. profile             ");        if (!profile1_empty) fprintf(stdout,"(loaded)");        fprintf(stdout,"\n");        fprintf(stdout,"    2.  Input 2nd. profile/sequences   ");        if (!profile2_empty) fprintf(stdout,"(loaded)");        fprintf(stdout,"\n\n");        fprintf(stdout,"    3.  Align 2nd. profile to 1st. profile\n");        fprintf(stdout,"    4.  Align sequences to 1st. profile (%s)\n\n",                        (!quick_pairalign) ? "Slow/Accurate" : "Fast/Approximate");        fprintf(stdout,"    5.  Toggle Slow/Fast pairwise alignments = %s\n\n",                                        (!quick_pairalign) ? "SLOW" : "FAST");        fprintf(stdout,"    6.  Pairwise alignment parameters\n");        fprintf(stdout,"    7.  Multiple alignment parameters\n\n");        fprintf(stdout,"    8.  Toggle screen display                = %s\n",                                        (!showaln) ? "OFF" : "ON");        fprintf(stdout,"    9.  Output format options\n");        fprintf(stdout,"    0.  Secondary structure options\n");        fprintf(stdout,"\n");        fprintf(stdout,"    S.  Execute a system command\n");        fprintf(stdout,"    H.  HELP\n");        fprintf(stdout,"    or press [RETURN] to go back to main menu\n\n\n");        getstr("Your choice",lin1);        if(*lin1 == EOS) return;        switch(toupper(*lin1))        {        case '1': profile_no = 1;      /* 1 => 1st profile */           profile_input();		  strcpy(profile1_name, seqname);            break;        case '2': profile_no = 2;      /* 2 => 2nd profile */          profile_input();		  strcpy(profile2_name, seqname);            break;        case '3': profile_align(p1_tree_name,p2_tree_name);       /* align the 2 alignments now */            break;        case '4': new_sequence_align(phylip_name);  /* align new sequences to profile 1 */            break;        case '5': quick_pairalign ^= TRUE;	    break;        case '6': pair_menu();            break;        case '7': multi_menu();            break;        case '8': showaln ^= TRUE;	    break;        case '9': format_options_menu();            break;        case '0': ss_options_menu();            break;        case 'S': do_system();            break;        case '?':        case 'H': get_help('6');            break;        case 'Q':        case 'X': return;        default: fprintf(stdout,"\n\nUnrecognised Command\n\n");            break;        }    }}static void ss_options_menu(void){        int catchint;        catchint = signal(SIGINT, SIG_IGN) != SIG_IGN;        if (catchint) {                if (setjmp(jmpbuf) != 0)                        fprintf(stdout,"\n.. Interrupt\n");#ifdef UNIX                if (signal(SIGINT,jumper) == BADSIG)                        fprintf(stdout,"Error: signal\n");#else                if (signal(SIGINT,SIG_DFL) == BADSIG)                        fprintf(stdout,"Error: signal\n");#endif        }	while(TRUE) {			fprintf(stdout,"\n\n\n");		fprintf(stdout," ********* SECONDARY STRUCTURE OPTIONS *********\n");		fprintf(stdout,"\n\n");		fprintf(stdout,"     1. Use profile 1 secondary structure / penalty mask  ");		if(use_ss1)			fprintf(stdout,"= YES\n");		else			fprintf(stdout,"= NO\n");		fprintf(stdout,"     2. Use profile 2 secondary structure / penalty mask  ");		if(use_ss2)			fprintf(stdout,"= YES\n");		else